Deinococcus radiodurans is known for its extreme resistance to ionizing radiation, oxidative stress, and other DNA-damaging agents. The robustness of this bacterium primarily originates from its strong oxidative resistance mechanisms. Hundreds of genes have been demonstrated to contribute to oxidative resistance in D. radiodurans; however, the antioxidant mechanisms have not been fully characterized. In this study, comparative proteomics analysis of D. radiodurans grown under normal and oxidative stress conditions was conducted using label-free quantitative proteomics. The abundances of 852 of 1700 proteins were found to significantly differ between the two groups. These differential proteins are mainly associated with translation, DNA repair and recombination, response to stresses, transcription, and cell wall organization. Highly upregulated expression was observed for ribosomal proteins such as RplB, Rpsl, RpsR, DNA damage response proteins (DdrA, DdrB), DNA repair proteins (RecN, RecA), and transcriptional regulators (members of TetR, AsnC, and GntR families, DdrI). The functional analysis of proteins in response to oxidative stress is discussed in detail. This study reveals the global protein expression profile of D. radiodurans in response to oxidative stress and provides new insights into the regulatory mechanism of oxidative resistance in D. radiodurans.

Members of the Microvirga genus are metabolically versatile and widely distributed in Nature. However, knowledge of the bacteria that belong to this genus is currently limited to biochemical characteristics. Herein, a novel thermo-tolerant bacterium named Microvirga thermotolerans HR1 was isolated and identified. Based on the 16S rRNA gene sequence analysis, the strain HR1 belonged to the genus Microvirga and was highly similar to Microvirga sp. 17 mud 1-3. The strain could grow at temperatures ranging from 15 to 50 °C with a growth optimum at 40 °C. It exhibited tolerance to pH range of 6.0–8.0 and salt concentrations up to 0.5% (w/v). It contained ubiquinone 10 as the predominant quinone and added group 8 as the main fatty acids. Analysis of 11 whole genomes of Microvirga species revealed that Microvirga segregated into two main distinct clades (soil and root nodule) as affected by the isolation source. Members of the soil clade had a high ratio of heat- or radiation-resistant genes, whereas members of the root nodule clade were characterized by a significantly higher abundance of genes involved in symbiotic nitrogen fixation or nodule formation. The taxonomic clustering of Microvirga strains indicated strong functional differentiation and niche-specific adaption.

Deinococcus radiodurans adapts to challenging environments by modulating gene expression in response to oxidative stress. Recently, bacterial small noncoding RNAs (sRNAs) have been presumed to participate in the transcriptional or translational regulation of stress-responsive genes. We found 24 sRNAs that may be involved in the oxidative stress response of D. radiodurans by deep RNA sequencing. Moreover, a typical stress-inducible sRNA, IGR_3053, named OsiA, was predicted to bind to the mRNA of katA, katE, and sodC by the bioinformatics method. An osiA knockout of D. radiodurans displayed increased sensitivity to H₂O₂ and the decreased catalase activity and total antioxidant activity, suggesting that OsiA probably serves as a regulator in the adaptation to oxidative environments. Further microscale thermophoresis results demonstrated that OsiA can directly bind to the mRNA of katA, sodC, and katE. The stability test result of katA mRNA showed that its half-life was 2 min in the osiA mutant compared with 5 min in the wildtype(wt) strain. Our results indicated that OsiA can enhance the stability of katA mRNA and the activity of KatA and consequently the oxidation resistance of D.radiodurans. We are the first one to explore the super-strong oxidative stress resistance of D.radiodurans at the level of post-transcriptional regulation, and found a new pathway that provides a new explanation for the long-term adaptability of D.radiodurans in extreme environments.

A Gram-stain-negative, short rod-shaped, non-motile, non-spore-forming bacterial strain, designated H7^T, was isolated from the Gobi desert, Xinjiang Province of China. The temperature, NaCl and pH ranges for growth were 8–40 °C (optimum 30 °C), 0–5 % (w/v) NaCl and pH 6–10 (optimum pH 7), respectively. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain H7^T belonged to the genus Sphingobacterium and showed highest sequence similarity (91 %) to Sphingobacterium composti DSM 18850. The genomic DNA G+C content was 44.3 mol%. MK-7 was identified as the predominant respiratory quinone. Strain H7^T contained C_16 : 1ω7c and/or C_16 : 1ω6c, iso-C_15 : 0 and iso-C_17 : 0 3-OH as major fatty acids. These data support the affiliation of strain H7^T to the genus Sphingobacterium while phenotypic data indicated it is a representative strain of a novel species for which the name Sphingobacterium gobiense sp. nov. is proposed. The type strain is H7^T ( = ACCC 05757^T = KCTC 32293^T).

Deinococcus radiodurans is a polyextremophilic bacterium well known for its extreme resistance to irradiation, oxidative stress, and other damaging conditions. Many small noncoding RNAs (ncRNAs) in D. radiodurans have been identified by deep sequencing analysis and computational predictions. However, the precise roles of ncRNAs and their target genes in the oxidative stress response have not been investigated. Here, we report the identification and characterization of a novel ncRNA named OsiR (for oxidative stress-induced ncRNA). Oxidative stress tolerance analysis showed that deleting osiR significantly decreased viability, total antioxidant capacity, and catalase activity in D. radiodurans under oxidative stress conditions. Comparative phenotypic and qRT-PCR analyses of an osiR mutant identify a role of OsiR in regulating the expression of the catalase gene katE2. Microscale thermophoresis and genetic complementation showed that a 21-nt sequence in the stem–loop structure of OsiR (204–244 nt) directly base pairs with its counterpart in the coding region of katE2 mRNA (843–866 nt) via a 19 nt region. In addition, deletion of katE2 caused a significant reduction of catalase activity and oxidative stress tolerance similar to that observed in an osiR mutant. Our results show that OsiR positively regulates oxidative stress tolerance in D. radiodurans by increasing the mRNA stability and translation efficiency of katE2. This work provides a new regulatory pathway mediated by ncRNA for the oxidative stress response that most likely contributes to the extreme tolerances of D. radiodurans.

A Gram-stain-negative, non-motile, heterotrophic, rod-shaped bacterium, designated strain W402^T, was isolated from an enrichment culture of a Tamarix ramosissima rhizosphere soil sample from the Xinjiang desert in the PR China. Analysis of the almost-complete 16S rRNA gene sequence showed that the isolate was phylogenetically related to a species of the genus Falsirhodobacter , having a close relationship to Falsirhodobacter halotolerans JA744^T (97 % similarity). However, DNA–DNA relatedness between W402^T and F. halotolerans JA744^T was 43.2±1.2 %. Strain W402^T grew in 0–10 % (w/v) NaCl. The temperature and pH ranges for growth were 10–40 °C and pH 5.5–10.0, respectively. Optimal growth occurred at 1–3 % (w/v) NaCl, 30 °C and pH 7.0. The predominant cellular fatty acids were summed feature 8 (C_18 : 1ω7c and/or C_18 : 1ω6c, 61.4 %), C_18 : 0 (9.8 %) and 11-methyl C_18 : 1ω7c (8.2 %). The major quinone of strain W402^T was Q-10. Phosphatidylethanolamine was predominant in the polar lipid profile. The DNA G+C content of strain W402^T was 67.3 mol%. Taken together, these results confirm that W402^T represents a novel species of the genus Falsirhodobacter , for which the name Falsirhodobacter deserti sp. nov. is proposed. The type strain is W402^T ( = ACCC 05851^T = KCTC 32408^T).